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BioEssays : News and Reviews in... Sep 2023Fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli, suggest a new view of protein fold space. For decades,...
Fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli, suggest a new view of protein fold space. For decades, experimental evidence has indicated that protein fold space is discrete: dissimilar folds are encoded by dissimilar amino acid sequences. Challenging this assumption, fold-switching proteins interconnect discrete groups of dissimilar protein folds, making protein fold space fluid. Three recent observations support the concept of fluid fold space: (1) some amino acid sequences interconvert between folds with distinct secondary structures, (2) some naturally occurring sequences have switched folds by stepwise mutation, and (3) fold switching is evolutionarily selected and likely confers advantage. These observations indicate that minor amino acid sequence modifications can transform protein structure and function. Consequently, proteomic structural and functional diversity may be expanded by alternative splicing, small nucleotide polymorphisms, post-translational modifications, and modified translation rates.
Topics: Protein Folding; Proteomics; Models, Molecular; Proteins; Amino Acid Sequence
PubMed: 37431685
DOI: 10.1002/bies.202300057 -
The Journal of Biological Chemistry Nov 2023p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin... (Review)
Review
p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin regulation. Dysregulation of p97 function causes severe neurodegenerative disease and is associated with cancer, making this protein a significant therapeutic target. p97 extracts polypeptide substrates from macromolecular assemblies by hydrolysis-driven translocation through its central pore. Growing evidence indicates that this activity is highly coordinated by "adapter" partner proteins, of which more than 30 have been identified and are commonly described to facilitate translocation through substrate recruitment or modification. In so doing, these adapters enable critical p97-dependent functions such as extraction of misfolded proteins from the endoplasmic reticulum or mitochondria, and are likely the reason for the extreme functional diversity of p97 relative to other AAA+ translocases. Here, we review the known functions of adapter proteins and highlight recent structural and biochemical advances that have begun to reveal the diverse molecular bases for adapter-mediated regulation of p97 function. These studies suggest that the range of mechanisms by which p97 activity is controlled is vastly underexplored with significant advances possible for understanding p97 regulation by the most known adapters.
Topics: Humans; Adaptor Proteins, Signal Transducing; Valosin Containing Protein; Protein Folding; Protein Domains; Models, Molecular; Protein Structure, Quaternary
PubMed: 37611827
DOI: 10.1016/j.jbc.2023.105182 -
Current Opinion in Structural Biology Jun 2024In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which... (Review)
Review
In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which reversibly interconvert between multiple, sometimes highly dissimilar, native states. As the number of known metamorphic proteins increases, several computational and experimental strategies have emerged for gaining insights about their refolding processes and identifying unknown metamorphic proteins amongst the known proteome. In this review, we describe the current advances in biophysically and functionally ascertaining the structural interconversions of metamorphic proteins and how coevolution can be harnessed to identify novel metamorphic proteins from sequence information. We also discuss the challenges and ongoing efforts in using artificial intelligence-based protein structure prediction methods to discover metamorphic proteins and predict their corresponding three-dimensional structures.
Topics: Proteins; Protein Folding; Protein Conformation; Models, Molecular; Humans; Artificial Intelligence
PubMed: 38537533
DOI: 10.1016/j.sbi.2024.102807 -
ACS Chemical Biology Jul 2023Disulfide bonds form covalent bonds between distal regions of peptides and proteins to dramatically impact their folding, stability, and oligomerization. Given the...
Disulfide bonds form covalent bonds between distal regions of peptides and proteins to dramatically impact their folding, stability, and oligomerization. Given the prevalence of disulfide bonds in many natural products, considerable effort has been invested in site-selective disulfide bond formation approaches to control the folding of chemically synthesized peptides and proteins. Here, we show that the careful choice of thiol oxidation conditions can lead to monomeric or dimeric species from fully deprotected linear bisthiol peptides. Starting from a p53-derived peptide, we found that oxidation under aqueous (nondenaturing) conditions produces antiparallel dimers with enhanced α-helical character, while oxidation under denaturing conditions promotes formation of a nonhelical intramolecular disulfide species. Examination across peptide variants suggests that intramolecular disulfide formation is robust across diverse peptide sequences, while dimerization is sensitive to both the α-helical folding of the linear peptide and aromatic residues at the dimerization interface. All disulfide species are more resistant to protease degradation than the linear peptide but are easily reduced to restore the initial bisthiol peptide. Both disulfide formation approaches are compatible with α-helix-stabilizing cross-linkers. These results provide an approach for using disulfide bonds to control peptide folding and oligomerization to better understand how folding influences interactions with diverse molecular targets.
Topics: Disulfides; Protein Folding; Dimerization; Proteins; Peptides; Oxidation-Reduction
PubMed: 37390465
DOI: 10.1021/acschembio.3c00268 -
Biochimica Et Biophysica Acta.... Jan 2024Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the... (Review)
Review
Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the last new class of antibiotics active against these bacteria was introduced to the clinic over 60 years ago, thus there is an immediate unmet need for new antibiotic classes able to overcome resistance. The outer membrane, a unique and essential structure in gram-negative bacteria, contains multiple potential antibacterial targets including BamA, an outer membrane protein that folds and inserts transmembrane β-barrel proteins. BamA is essential and conserved, and its outer membrane location eliminates a barrier that molecules must overcome to access this target. Recently, antibacterial small molecules, natural products, peptides, and antibodies that inhibit BamA activity have been reported, validating the druggability of this target and generating potential leads for antibiotic development. This review will describe these BamA inhibitors, highlight their key attributes, and identify challenges with this potential target.
Topics: Humans; Escherichia coli Proteins; Escherichia coli; Protein Folding; Bacterial Outer Membrane Proteins; Gram-Negative Bacteria; Anti-Bacterial Agents
PubMed: 37852326
DOI: 10.1016/j.bbamcr.2023.119609 -
Molecular Cell Nov 2023The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins...
The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determine the structures of human CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ, a component of Regulator of G protein Signaling (RGS) complexes. Cryoelectron microscopy (cryo-EM) and image processing reveal an ensemble of distinct snapshots that represent the folding trajectory of Gβ from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT orchestrates folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
Topics: Humans; Cryoelectron Microscopy; Molecular Chaperones; GTP-Binding Proteins; Protein Folding; Signal Transduction; Chaperonins
PubMed: 37852256
DOI: 10.1016/j.molcel.2023.09.032 -
Nature Nov 2023Three billion years of evolution has produced a tremendous diversity of protein molecules, but the full potential of proteins is likely to be much greater. Accessing...
Three billion years of evolution has produced a tremendous diversity of protein molecules, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.
Topics: Humans; Algorithms; Bayes Theorem; Computer Simulation; Directed Molecular Evolution; Machine Learning; Models, Molecular; Protein Conformation; Protein Folding; Proteins; Semantics; Synthetic Biology
PubMed: 37968394
DOI: 10.1038/s41586-023-06728-8 -
Current Opinion in Structural Biology Dec 2023Proteins carry out the vast majority of functions in cells, but can only do so when properly folded. Following stress or mutation, proteins can lose their proper fold,... (Review)
Review
Proteins carry out the vast majority of functions in cells, but can only do so when properly folded. Following stress or mutation, proteins can lose their proper fold, resulting in misfolding, inactivity, and aggregation-posing a threat to cellular health. In order to counteract protein aggregation, cells have evolved a remarkable subset of molecular chaperones, called protein disaggregases, which collaboratively possess the ability to forcibly untangle protein aggregates. Here, we review the different chaperone disaggregation machineries present in the human cytosol and their mechanisms of action. Understanding, how these disaggregases function, is both universally and clinically important, as protein aggregation has been linked to multiple, debilitating neurodegenerative diseases.
Topics: Humans; HSP70 Heat-Shock Proteins; Cytosol; Protein Aggregates; Molecular Chaperones; Protein Folding
PubMed: 38000128
DOI: 10.1016/j.sbi.2023.102735 -
EMBO Reports Apr 2024Teratozoospermia is a significant cause of male infertility, but the pathogenic mechanism of acephalic spermatozoa syndrome (ASS), one of the most severe...
Teratozoospermia is a significant cause of male infertility, but the pathogenic mechanism of acephalic spermatozoa syndrome (ASS), one of the most severe teratozoospermia, remains elusive. We previously reported Spermatogenesis Associated 6 (SPATA6) as the component of the sperm head-tail coupling apparatus (HTCA) required for normal assembly of the sperm head-tail conjunction, but the underlying molecular mechanism has not been explored. Here, we find that the co-chaperone protein BAG5, expressed in step 9-16 spermatids, is essential for sperm HTCA assembly. BAG5-deficient male mice show abnormal assembly of HTCA, leading to ASS and male infertility, phenocopying SPATA6-deficient mice. In vivo and in vitro experiments demonstrate that SPATA6, cargo transport-related myosin proteins (MYO5A and MYL6) and dynein proteins (DYNLT1, DCTN1, and DNAL1) are misfolded upon BAG5 depletion. Mechanistically, we find that BAG5 forms a complex with HSPA8 and promotes the folding of SPATA6 by enhancing HSPA8's affinity for substrate proteins. Collectively, our findings reveal a novel protein-regulated network in sperm formation in which BAG5 governs the assembly of the HTCA by activating the protein-folding function of HSPA8.
Topics: Animals; Humans; Male; Mice; Adaptor Proteins, Signal Transducing; Cytoskeletal Proteins; Dyneins; HSC70 Heat-Shock Proteins; Infertility, Male; Molecular Chaperones; Protein Folding; Semen; Sperm Head; Spermatogenesis; Spermatozoa; Teratozoospermia; Thiazoles
PubMed: 38454159
DOI: 10.1038/s44319-024-00112-x -
Briefings in Bioinformatics Sep 2023For refining and designing protein structures, it is essential to have an efficient protein folding and docking framework that generates a protein 3D structure based on...
For refining and designing protein structures, it is essential to have an efficient protein folding and docking framework that generates a protein 3D structure based on given constraints. In this study, we introduce OPUS-Fold3 as a gradient-based, all-atom protein folding and docking framework, which accurately generates 3D protein structures in compliance with specified constraints, such as a potential function as long as it can be expressed as a function of positions of heavy atoms. Our tests show that, for example, OPUS-Fold3 achieves performance comparable to pyRosetta in backbone folding and significantly better in side-chain modeling. Developed using Python and TensorFlow 2.4, OPUS-Fold3 is user-friendly for any source-code level modifications and can be seamlessly combined with other deep learning models, thus facilitating collaboration between the biology and AI communities. The source code of OPUS-Fold3 can be downloaded from http://github.com/OPUS-MaLab/opus_fold3. It is freely available for academic usage.
Topics: Models, Molecular; Proteins; Software; Protein Folding
PubMed: 37833840
DOI: 10.1093/bib/bbad365